Wed Feb 15 08:55:42 PST 2012 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph_thinner.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:42 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6655077 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 0.6655077 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.16734 92.64875 91.29704 assigned negative charge : -312.5923 centred at (gu) : 90.21777 92.47301 91.28671 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6672 nv = 96 ne = 84 npr = 44296 no. pairs analyzed = 44296 no. exposed pairs = 2987 no. arc points = 21356 no. surface atoms = 995 nbur = 1185 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3416 m= 6 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3300000 number of dielectric boundary points 3615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1938 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2507432E-09 6.9260366E-09 midg,1,midg; midg,igrid,midg -1.6702874E-08 6.1132731E-08 1,midg,midg; igrid,midg,midg 1.2142614E-08 -5.9799521E-09 gauss-seidel spectral radius is 0.9882691 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 08:55:43 rms-change max change #iterations 0.1547049 22.26619 at 10iterations 1.6681259E-02 2.459642 at 20iterations 1.7725177E-03 0.2669792 at 30iterations 1.9141579E-04 2.8146744E-02 at 40iterations 2.0808910E-05 3.0835867E-03 at 50iterations finished qdiffx linear iterations at : 08:55:46 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.0808910E-05 3.0835867E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:55:47 3.500u 0.163s 0:04.58 79.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:47 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.996523 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 1.996523 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.50178 97.94637 93.89090 assigned negative charge : -312.5923 centred at (gu) : 90.65359 97.41942 93.86034 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21356 grid for indexing accessible points = 1.400000 m= 25771 mr = 46224 m= 4791 mr = 18662 m= 395 mr = 3128 m= 6 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 33140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16166 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6655077 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7497916E-02 4.9888127E-02 midg,1,midg; midg,igrid,midg -5.0655673E-03 6.4929910E-02 1,midg,midg; igrid,midg,midg -1.8672785E-02 -3.2808226E-02 gauss-seidel spectral radius is 0.9987199 estimated iterations to convergence 221 setup time was (sec) 0.8900000 now iterating at: 08:55:48 rms-change max change #iterations 4.127944 232.3250 at 10iterations 1.980857 79.80161 at 20iterations 0.9515111 32.57880 at 30iterations 0.4571482 14.97128 at 40iterations 0.2196041 7.291463 at 50iterations 0.1054488 3.526278 at 60iterations 5.0660480E-02 1.735065 at 70iterations 2.4302956E-02 0.7793283 at 80iterations 1.1623239E-02 0.4188285 at 90iterations 5.5908044E-03 0.1839080 at 100iterations 2.6799666E-03 8.9225769E-02 at 110iterations 1.2862997E-03 4.6553612E-02 at 120iterations finished qdiffx linear iterations at : 08:55:56 total time elapsed so far: 8.690000 # loops : 120 mean,max change (kT/e) : 1.2862997E-03 4.6553612E-02 energy calculations done at 8.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 08:55:57 8.890u 0.243s 0:09.87 92.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.994785 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 2.994785 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.75258 101.9194 95.83628 assigned negative charge : -312.5923 centred at (gu) : 90.98042 101.1292 95.79047 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162661 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21356 grid for indexing accessible points = 1.400000 m= 80220 mr = 112721 m= 31511 mr = 64221 m= 8922 mr = 25412 m= 1623 mr = 6727 m= 107 mr = 1175 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 74748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 16340 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.996523 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1507502E-02 0.5020881 midg,1,midg; midg,igrid,midg -7.4642211E-02 0.4638934 1,midg,midg; igrid,midg,midg -0.2576618 -0.3070351 gauss-seidel spectral radius is 0.9992891 estimated iterations to convergence 296 setup time was (sec) 1.780000 now iterating at: 08:55:59 rms-change max change #iterations 9.513514 478.5066 at 10iterations 5.572187 163.8120 at 20iterations 3.260807 64.81016 at 30iterations 1.906058 46.63592 at 40iterations 1.111703 25.19976 at 50iterations 0.6465425 11.96034 at 60iterations 0.3760029 7.172737 at 70iterations 0.2180657 4.270332 at 80iterations 0.1268008 2.223537 at 90iterations 7.3587760E-02 1.353820 at 100iterations 4.2645663E-02 0.8020802 at 110iterations 2.4791101E-02 0.4594612 at 120iterations 1.4419950E-02 0.2588043 at 130iterations 8.3606848E-03 0.1610405 at 140iterations 4.8632724E-03 8.6826324E-02 at 150iterations 2.8209882E-03 5.1333427E-02 at 160iterations 1.6376023E-03 2.7803421E-02 at 170iterations 9.4829121E-04 1.6935349E-02 at 180iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 9.4829121E-04 1.6935349E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:56:11 13.314u 0.237s 0:14.24 95.0% 0+0k 0+0io 0pf+0w